Starting phenix.real_space_refine on Fri Apr 5 19:02:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo7_32641/04_2024/7wo7_32641.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo7_32641/04_2024/7wo7_32641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo7_32641/04_2024/7wo7_32641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo7_32641/04_2024/7wo7_32641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo7_32641/04_2024/7wo7_32641.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo7_32641/04_2024/7wo7_32641.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3069 2.51 5 N 816 2.21 5 O 965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 98": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "B" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "C" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1550 Unusual residues: {'NAG': 1} Classifications: {'peptide': 194, 'undetermined': 1} Link IDs: {'PTRANS': 11, 'TRANS': 182, None: 1} Not linked: pdbres="PRO C 527 " pdbres="NAG C 601 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.16, per 1000 atoms: 0.65 Number of scatterers: 4870 At special positions: 0 Unit cell: (74.9, 95.23, 107, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 965 8.00 N 816 7.00 C 3069 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 91 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 960.5 milliseconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1168 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 13 sheets defined 5.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.625A pdb=" N LYS A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.520A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.516A pdb=" N ASP B 85 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 86 " --> pdb=" O THR B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 82 through 86' Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.876A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.709A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.222A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.797A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 5 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 7 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 20 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.986A pdb=" N GLY A 10 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 34 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 36 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 59 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.986A pdb=" N GLY A 10 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.654A pdb=" N SER A 186 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 185 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 172 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 187 " --> pdb=" O HIS A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.127A pdb=" N VAL B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 107 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.127A pdb=" N VAL B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 107 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 102 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.743A pdb=" N ILE B 20 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 197 through 199 removed outlier: 3.586A pdb=" N CYS B 199 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS B 210 " --> pdb=" O CYS B 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.873A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.602A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.582A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 153 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1472 1.33 - 1.45: 883 1.45 - 1.57: 2618 1.57 - 1.70: 0 1.70 - 1.82: 23 Bond restraints: 4996 Sorted by residual: bond pdb=" C GLN B 114 " pdb=" N PRO B 115 " ideal model delta sigma weight residual 1.326 1.387 -0.061 1.44e-02 4.82e+03 1.79e+01 bond pdb=" CA GLN B 114 " pdb=" C GLN B 114 " ideal model delta sigma weight residual 1.523 1.558 -0.035 1.25e-02 6.40e+03 7.77e+00 bond pdb=" C GLU A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.333 1.351 -0.018 7.80e-03 1.64e+04 5.42e+00 bond pdb=" N ALA A 120 " pdb=" CA ALA A 120 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.27e+00 bond pdb=" C TYR B 146 " pdb=" N PRO B 147 " ideal model delta sigma weight residual 1.332 1.356 -0.025 1.30e-02 5.92e+03 3.56e+00 ... (remaining 4991 not shown) Histogram of bond angle deviations from ideal: 100.63 - 107.30: 199 107.30 - 113.97: 2743 113.97 - 120.64: 1836 120.64 - 127.31: 1974 127.31 - 133.98: 59 Bond angle restraints: 6811 Sorted by residual: angle pdb=" C GLN B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta sigma weight residual 120.98 115.18 5.80 1.07e+00 8.73e-01 2.94e+01 angle pdb=" C PRO A 153 " pdb=" N GLU A 154 " pdb=" CA GLU A 154 " ideal model delta sigma weight residual 122.28 118.32 3.96 1.02e+00 9.61e-01 1.51e+01 angle pdb=" N THR A 197 " pdb=" CA THR A 197 " pdb=" C THR A 197 " ideal model delta sigma weight residual 112.68 107.71 4.97 1.33e+00 5.65e-01 1.40e+01 angle pdb=" N ALA A 120 " pdb=" CA ALA A 120 " pdb=" C ALA A 120 " ideal model delta sigma weight residual 110.80 118.23 -7.43 2.13e+00 2.20e-01 1.22e+01 angle pdb=" N LYS C 378 " pdb=" CA LYS C 378 " pdb=" C LYS C 378 " ideal model delta sigma weight residual 108.17 114.22 -6.05 1.85e+00 2.92e-01 1.07e+01 ... (remaining 6806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 2797 16.83 - 33.66: 130 33.66 - 50.49: 41 50.49 - 67.32: 10 67.32 - 84.15: 2 Dihedral angle restraints: 2980 sinusoidal: 1145 harmonic: 1835 Sorted by residual: dihedral pdb=" N ALA A 120 " pdb=" C ALA A 120 " pdb=" CA ALA A 120 " pdb=" CB ALA A 120 " ideal model delta harmonic sigma weight residual 122.90 132.46 -9.56 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" C ALA A 120 " pdb=" N ALA A 120 " pdb=" CA ALA A 120 " pdb=" CB ALA A 120 " ideal model delta harmonic sigma weight residual -122.60 -131.98 9.38 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" CB GLU B 189 " pdb=" CG GLU B 189 " pdb=" CD GLU B 189 " pdb=" OE1 GLU B 189 " ideal model delta sinusoidal sigma weight residual 0.00 -84.15 84.15 1 3.00e+01 1.11e-03 9.58e+00 ... (remaining 2977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 676 0.073 - 0.145: 71 0.145 - 0.218: 2 0.218 - 0.290: 0 0.290 - 0.363: 1 Chirality restraints: 750 Sorted by residual: chirality pdb=" CA ALA A 120 " pdb=" N ALA A 120 " pdb=" C ALA A 120 " pdb=" CB ALA A 120 " both_signs ideal model delta sigma weight residual False 2.48 2.12 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA LYS C 378 " pdb=" N LYS C 378 " pdb=" C LYS C 378 " pdb=" CB LYS C 378 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA TYR C 369 " pdb=" N TYR C 369 " pdb=" C TYR C 369 " pdb=" CB TYR C 369 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 747 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 190 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO A 191 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 27 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C GLY B 27 " 0.027 2.00e-02 2.50e+03 pdb=" O GLY B 27 " -0.010 2.00e-02 2.50e+03 pdb=" N SER B 28 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 125 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO B 126 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " -0.019 5.00e-02 4.00e+02 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 207 2.71 - 3.26: 4598 3.26 - 3.81: 7752 3.81 - 4.35: 9274 4.35 - 4.90: 15771 Nonbonded interactions: 37602 Sorted by model distance: nonbonded pdb=" O LYS B 155 " pdb=" OG SER B 198 " model vdw 2.163 2.440 nonbonded pdb=" OG1 THR B 122 " pdb=" O LEU B 141 " model vdw 2.254 2.440 nonbonded pdb=" O ARG C 408 " pdb=" NE2 GLN C 414 " model vdw 2.266 2.520 nonbonded pdb=" O ALA B 163 " pdb=" OG SER B 185 " model vdw 2.277 2.440 nonbonded pdb=" O SER B 13 " pdb=" NZ LYS B 16 " model vdw 2.315 2.520 ... (remaining 37597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 21.390 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 17.340 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4996 Z= 0.194 Angle : 0.706 7.428 6811 Z= 0.447 Chirality : 0.044 0.363 750 Planarity : 0.004 0.042 882 Dihedral : 11.244 84.155 1788 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 8.82 % Allowed : 7.17 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.28), residues: 628 helix: -4.77 (0.47), residues: 12 sheet: -2.88 (0.35), residues: 172 loop : -3.42 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 33 HIS 0.001 0.000 HIS A 206 PHE 0.009 0.001 PHE C 400 TYR 0.010 0.001 TYR C 369 ARG 0.001 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 143 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8329 (mt0) REVERT: A 184 LEU cc_start: 0.6631 (tp) cc_final: 0.6263 (tp) REVERT: A 212 LYS cc_start: 0.6387 (mmtt) cc_final: 0.5984 (mmtt) REVERT: B 29 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8955 (tt) REVERT: B 113 SER cc_start: 0.6507 (OUTLIER) cc_final: 0.6204 (p) REVERT: B 168 THR cc_start: 0.5662 (OUTLIER) cc_final: 0.5215 (p) REVERT: B 189 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6904 (mm-30) REVERT: B 190 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.6037 (tt0) REVERT: B 192 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.5021 (mmmt) REVERT: B 194 HIS cc_start: 0.6438 (OUTLIER) cc_final: 0.6054 (m90) REVERT: B 195 ARG cc_start: 0.6583 (mmm160) cc_final: 0.5683 (mpp-170) REVERT: C 356 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7948 (tptp) REVERT: C 378 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8526 (mmmt) REVERT: C 394 ASN cc_start: 0.7748 (m-40) cc_final: 0.7288 (m-40) REVERT: C 452 LEU cc_start: 0.8394 (mt) cc_final: 0.8036 (mp) REVERT: C 516 GLU cc_start: 0.6658 (pt0) cc_final: 0.6439 (pt0) REVERT: C 517 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7591 (tm) outliers start: 48 outliers final: 15 residues processed: 177 average time/residue: 0.2047 time to fit residues: 44.2904 Evaluate side-chains 105 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 80 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 517 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 48 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS B 92 GLN B 99 HIS B 100 ASN B 190 GLN ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 409 GLN C 439 ASN C 474 GLN C 481 ASN C 493 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4996 Z= 0.262 Angle : 0.613 7.730 6811 Z= 0.318 Chirality : 0.046 0.274 750 Planarity : 0.005 0.081 882 Dihedral : 9.468 83.100 767 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 7.90 % Allowed : 13.05 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.29), residues: 628 helix: -4.43 (0.75), residues: 18 sheet: -2.35 (0.36), residues: 190 loop : -3.18 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 36 HIS 0.002 0.001 HIS B 99 PHE 0.019 0.002 PHE C 400 TYR 0.015 0.002 TYR A 182 ARG 0.003 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 97 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7122 (t0) cc_final: 0.6636 (t70) REVERT: A 147 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.5725 (mp) REVERT: A 184 LEU cc_start: 0.6879 (tp) cc_final: 0.6581 (tp) REVERT: B 189 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: B 194 HIS cc_start: 0.6657 (OUTLIER) cc_final: 0.6404 (m90) REVERT: B 195 ARG cc_start: 0.6424 (mmm160) cc_final: 0.5384 (mpp-170) REVERT: C 356 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8312 (tptp) REVERT: C 406 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6415 (tt0) REVERT: C 517 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7867 (tm) outliers start: 43 outliers final: 23 residues processed: 130 average time/residue: 0.1840 time to fit residues: 29.7600 Evaluate side-chains 99 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 70 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.0470 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 55 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4996 Z= 0.223 Angle : 0.593 6.706 6811 Z= 0.307 Chirality : 0.046 0.205 750 Planarity : 0.005 0.087 882 Dihedral : 8.208 83.037 747 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 6.99 % Allowed : 16.54 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.30), residues: 628 helix: -4.64 (0.60), residues: 18 sheet: -2.13 (0.35), residues: 201 loop : -3.03 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 353 HIS 0.008 0.001 HIS B 203 PHE 0.018 0.002 PHE C 400 TYR 0.011 0.002 TYR C 508 ARG 0.002 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 78 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7031 (t0) cc_final: 0.6583 (t70) REVERT: A 76 LYS cc_start: 0.8272 (pttp) cc_final: 0.7955 (pttm) REVERT: A 102 TYR cc_start: 0.9112 (t80) cc_final: 0.8907 (t80) REVERT: A 123 LYS cc_start: 0.8472 (pttt) cc_final: 0.8129 (pttm) REVERT: A 184 LEU cc_start: 0.6792 (tp) cc_final: 0.6583 (tp) REVERT: A 212 LYS cc_start: 0.6484 (mmtt) cc_final: 0.6253 (mmtt) REVERT: B 176 ASN cc_start: 0.6166 (m-40) cc_final: 0.5920 (t0) REVERT: B 195 ARG cc_start: 0.6533 (mmm160) cc_final: 0.5406 (mpp-170) REVERT: C 356 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8280 (tptp) REVERT: C 406 GLU cc_start: 0.6824 (tt0) cc_final: 0.6531 (tt0) REVERT: C 452 LEU cc_start: 0.8816 (mp) cc_final: 0.8527 (mt) outliers start: 38 outliers final: 25 residues processed: 109 average time/residue: 0.1973 time to fit residues: 26.9752 Evaluate side-chains 99 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 73 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 74 ASN B 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4996 Z= 0.323 Angle : 0.664 7.430 6811 Z= 0.341 Chirality : 0.046 0.234 750 Planarity : 0.005 0.086 882 Dihedral : 7.379 57.510 737 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.45 % Favored : 84.55 % Rotamer: Outliers : 7.17 % Allowed : 17.65 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.31), residues: 628 helix: -4.65 (0.60), residues: 18 sheet: -1.98 (0.36), residues: 200 loop : -3.00 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 353 HIS 0.006 0.002 HIS A 206 PHE 0.019 0.002 PHE C 400 TYR 0.012 0.002 TYR C 380 ARG 0.003 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 76 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.6576 (mmtt) cc_final: 0.6336 (mmtt) REVERT: B 51 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7221 (mt-10) REVERT: B 195 ARG cc_start: 0.6384 (mmm160) cc_final: 0.5302 (mpp-170) REVERT: C 356 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8454 (tptp) REVERT: C 406 GLU cc_start: 0.6845 (tt0) cc_final: 0.6449 (tt0) REVERT: C 409 GLN cc_start: 0.8082 (mt0) cc_final: 0.7691 (mp10) outliers start: 39 outliers final: 28 residues processed: 109 average time/residue: 0.1709 time to fit residues: 23.6456 Evaluate side-chains 95 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 66 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 501 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4996 Z= 0.249 Angle : 0.640 7.367 6811 Z= 0.328 Chirality : 0.046 0.204 750 Planarity : 0.005 0.090 882 Dihedral : 7.213 57.431 735 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.49 % Favored : 85.51 % Rotamer: Outliers : 7.35 % Allowed : 15.99 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.31), residues: 628 helix: -4.69 (0.57), residues: 18 sheet: -1.96 (0.36), residues: 204 loop : -2.82 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.005 0.001 HIS A 206 PHE 0.019 0.002 PHE C 400 TYR 0.010 0.001 TYR C 380 ARG 0.002 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 67 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 215 LYS cc_start: 0.6165 (pttp) cc_final: 0.5555 (pttp) REVERT: B 51 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7205 (mt-10) REVERT: B 114 GLN cc_start: 0.7399 (mp10) cc_final: 0.7122 (mp10) REVERT: B 154 TRP cc_start: 0.6278 (m-10) cc_final: 0.6064 (m-10) REVERT: B 195 ARG cc_start: 0.6356 (mmm160) cc_final: 0.5292 (mpp-170) REVERT: C 356 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8374 (tptp) outliers start: 40 outliers final: 29 residues processed: 98 average time/residue: 0.1847 time to fit residues: 22.9114 Evaluate side-chains 92 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 62 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 501 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4996 Z= 0.296 Angle : 0.675 10.315 6811 Z= 0.342 Chirality : 0.046 0.200 750 Planarity : 0.006 0.094 882 Dihedral : 7.443 58.111 735 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.92 % Favored : 84.08 % Rotamer: Outliers : 6.80 % Allowed : 17.65 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.32), residues: 628 helix: -4.68 (0.57), residues: 18 sheet: -2.02 (0.36), residues: 201 loop : -2.82 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.004 0.002 HIS A 206 PHE 0.022 0.002 PHE C 400 TYR 0.016 0.002 TYR C 489 ARG 0.003 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 67 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.6279 (pttp) cc_final: 0.5641 (pttp) REVERT: B 195 ARG cc_start: 0.6703 (mmm160) cc_final: 0.5496 (mpp-170) REVERT: C 356 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8444 (tptp) REVERT: C 452 LEU cc_start: 0.8728 (mp) cc_final: 0.8493 (tp) outliers start: 37 outliers final: 34 residues processed: 95 average time/residue: 0.1943 time to fit residues: 23.2796 Evaluate side-chains 94 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 59 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.0870 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4996 Z= 0.273 Angle : 0.662 8.034 6811 Z= 0.335 Chirality : 0.046 0.186 750 Planarity : 0.006 0.096 882 Dihedral : 7.338 57.154 735 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.61 % Favored : 84.39 % Rotamer: Outliers : 7.54 % Allowed : 17.83 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.32), residues: 628 helix: -4.71 (0.57), residues: 18 sheet: -1.90 (0.37), residues: 201 loop : -2.72 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.003 0.001 HIS A 206 PHE 0.027 0.002 PHE A 29 TYR 0.011 0.002 TYR C 489 ARG 0.002 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 66 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 215 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5780 (pttp) REVERT: B 114 GLN cc_start: 0.7253 (mp10) cc_final: 0.6947 (mp10) REVERT: B 176 ASN cc_start: 0.6126 (t0) cc_final: 0.5565 (t0) REVERT: B 195 ARG cc_start: 0.6604 (mmm160) cc_final: 0.5358 (mpp-170) REVERT: C 356 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8426 (tptp) REVERT: C 452 LEU cc_start: 0.8785 (mp) cc_final: 0.8553 (tp) outliers start: 41 outliers final: 36 residues processed: 97 average time/residue: 0.1870 time to fit residues: 23.1205 Evaluate side-chains 100 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 62 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4996 Z= 0.291 Angle : 0.674 7.804 6811 Z= 0.345 Chirality : 0.046 0.179 750 Planarity : 0.006 0.097 882 Dihedral : 7.422 55.240 735 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.56 % Favored : 83.44 % Rotamer: Outliers : 7.90 % Allowed : 17.10 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.32), residues: 628 helix: -4.67 (0.58), residues: 18 sheet: -1.87 (0.37), residues: 201 loop : -2.73 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.004 0.001 HIS A 206 PHE 0.020 0.002 PHE C 400 TYR 0.012 0.002 TYR B 89 ARG 0.002 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 63 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.6491 (OUTLIER) cc_final: 0.5780 (pttp) REVERT: B 195 ARG cc_start: 0.6580 (mmm160) cc_final: 0.5352 (mpp-170) REVERT: C 356 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8347 (tptp) outliers start: 43 outliers final: 37 residues processed: 95 average time/residue: 0.1894 time to fit residues: 22.9689 Evaluate side-chains 100 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 61 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 501 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.1980 chunk 43 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4996 Z= 0.249 Angle : 0.657 7.222 6811 Z= 0.334 Chirality : 0.046 0.185 750 Planarity : 0.005 0.098 882 Dihedral : 7.330 55.301 735 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.61 % Favored : 84.39 % Rotamer: Outliers : 7.35 % Allowed : 18.38 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.33), residues: 628 helix: -4.68 (0.58), residues: 18 sheet: -1.63 (0.39), residues: 195 loop : -2.62 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.004 0.001 HIS A 206 PHE 0.018 0.002 PHE C 400 TYR 0.018 0.002 TYR B 50 ARG 0.004 0.001 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 65 time to evaluate : 0.524 Fit side-chains REVERT: A 43 LYS cc_start: 0.7387 (mmmt) cc_final: 0.7174 (mmmt) REVERT: A 215 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.5750 (pttp) REVERT: B 114 GLN cc_start: 0.6878 (mp10) cc_final: 0.6507 (mt0) REVERT: B 195 ARG cc_start: 0.6535 (mmm160) cc_final: 0.5264 (mpp-170) REVERT: C 356 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8287 (tptp) REVERT: C 452 LEU cc_start: 0.8778 (mp) cc_final: 0.8576 (tp) outliers start: 40 outliers final: 35 residues processed: 95 average time/residue: 0.1700 time to fit residues: 20.7110 Evaluate side-chains 95 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 58 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 52 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4996 Z= 0.207 Angle : 0.625 7.185 6811 Z= 0.317 Chirality : 0.045 0.167 750 Planarity : 0.005 0.097 882 Dihedral : 7.116 57.330 735 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.65 % Favored : 85.35 % Rotamer: Outliers : 5.51 % Allowed : 20.40 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.33), residues: 628 helix: -4.64 (0.61), residues: 18 sheet: -1.41 (0.40), residues: 195 loop : -2.59 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 154 HIS 0.003 0.001 HIS A 206 PHE 0.015 0.001 PHE C 400 TYR 0.013 0.001 TYR C 489 ARG 0.003 0.000 ARG A 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 69 time to evaluate : 0.540 Fit side-chains REVERT: A 43 LYS cc_start: 0.7369 (mmmt) cc_final: 0.7153 (mmmt) REVERT: A 215 LYS cc_start: 0.6463 (OUTLIER) cc_final: 0.5799 (pttp) REVERT: B 114 GLN cc_start: 0.6662 (mp10) cc_final: 0.6348 (mt0) REVERT: B 116 LYS cc_start: 0.7276 (tmtt) cc_final: 0.6932 (tptt) REVERT: B 195 ARG cc_start: 0.6684 (mmm160) cc_final: 0.5365 (mpp-170) REVERT: C 356 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8195 (tptp) REVERT: C 429 PHE cc_start: 0.6192 (t80) cc_final: 0.5959 (t80) outliers start: 30 outliers final: 27 residues processed: 93 average time/residue: 0.1932 time to fit residues: 22.5554 Evaluate side-chains 95 residues out of total 544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 66 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.144050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.120565 restraints weight = 11823.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.119246 restraints weight = 9085.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.120376 restraints weight = 7692.417| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4996 Z= 0.301 Angle : 0.690 9.556 6811 Z= 0.348 Chirality : 0.046 0.175 750 Planarity : 0.006 0.097 882 Dihedral : 7.284 54.109 735 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.40 % Favored : 83.60 % Rotamer: Outliers : 6.07 % Allowed : 20.22 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.33), residues: 628 helix: -4.66 (0.59), residues: 18 sheet: -1.34 (0.39), residues: 195 loop : -2.68 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 154 HIS 0.004 0.001 HIS A 206 PHE 0.017 0.002 PHE C 400 TYR 0.019 0.002 TYR B 50 ARG 0.004 0.001 ARG A 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1727.70 seconds wall clock time: 32 minutes 13.62 seconds (1933.62 seconds total)